Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons

• Published in: Cell reports (Cambridge) 2023-11, Vol.42 (11), p.113335-113335, Article 113335
• Main Authors: Yang, Yalan, Yang, Runwei, Kang, Bowei, Qian, Sheng, He, Xin, Zhang, Xiaochang
• Format: Article
• Language: English
• Subjects: alternative splicing; Alternative Splicing - genetics; Autistic Disorder - genetics; coordinated splicing; CP: Molecular biology; CP: Neuroscience; de novo mutation; Exons - genetics; full-length transcripts; Humans; Introns - genetics; Protein Isoforms - genetics; retained intron; RNA Splice Sites; RNA Splicing - genetics; RNA-binding protein; scIso-seq; scRNA-seq; splice isoform; uncatalogued isoform
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.113335

Dysregulation of alternative splicing has been repeatedly associated with neurodevelopmental disorders, but the extent of cell-type-specific splicing in human neural development remains largely uncharted. Here, single-cell long-read sequencing in induced pluripotent stem cell (iPSC)-derived cerebral organoids identifies over 31,000 uncatalogued isoforms and 4,531 cell-type-specific splicing events. Long reads uncover coordinated splicing and cell-type-specific intron retention events, which are challenging to study with short reads. Retained neuronal introns are enriched in RNA splicing regulators, showing shorter lengths, higher GC contents, and weaker 5′ splice sites. We use this dataset to explore the biological processes underlying neurological disorders, focusing on autism. In comparison with prior transcriptomic data, we find that the splicing program in autistic brains is closer to the progenitor state than differentiated neurons. Furthermore, cell-type-specific exons harbor significantly more de novo mutations in autism probands than in siblings. Overall, these results highlight the importance of cell-type-specific splicing in autism and neuronal gene regulation. [Display omitted] •Over 31,000 uncatalogued isoforms are identified in human cerebral organoids•4,531 cell-type-specific splicing events are identified in human cerebral organoids•Alternative exons are enriched for autism-associated exons and de novo mutations•142 autism genes display cell-type-specific isoforms Yang et al. perform single-cell long-read sequencing in the human cerebral organoids, identifying thousands of uncatalogued isoforms, differentially spliced exons, and retained introns. Their results reveal the enrichement of autism-associated exons and de novo mutations in cell-type-specific exons.